Facebook may be gearing up for a big, new attack on the mobile market with the so-called Project Spartan, but first, a little housekeeping.

Over the last couple of days, the social network started to shut down dozens of applications that run on its platform — including some popular ones — seemingly without any notification to its developers, as it put in place a “new enforcement system” to respond to spam complaints from users. In the words of one developer, the move serves as a “great reminder of the power Facebook has over all of us developers.”

The news was first reported by the blog All Facebook, which noted that the shut downs appeared to affect mostly smaller applications with tens of thousands of daily active users. Blockbusters, like some of the social games published by the likes of Zynga, have millions of daily active users.

Some of the applications that were shut down, according to All Facebook, included Photo Effect (which says it has 7.5 million registered users, but only about 10,000 DAUs); Social Interview and Good Reads. We are contacting the publishers for verification of this.

On Friday, a Facebook engineer issued a statement on one of its own notice boards, explaining that Facebook had put a new enforcement system that took user feedback into account more than in the past:

We’ve been getting a lot of user feedback recently, spiking significantly over the past week, on the amount of application spam people are seeing in their feeds and on their walls. We turned on a new enforcement system yesterday that took user feedback much more heavily into account. This resulted in a number of applications with high negative user feedback being disabled or having certain features disabled. In particular, many applications were disabled which posted to the walls of other users and had very high mark-as-spam numbers.

My apologies for the suddenness of the action. The numbers were high enough to cause a real loss of trust in applications, which can impact the entire platform. Where we have failed is not providing enough feedback about negative engagement metrics to developers before needing to take this action. This is something we are working hard to fix with the new Application Insights that will be launching over the next few weeks – you will have detailed information about both positive and negative engagement of the content your application generates.

As of this today, it looks like many of the apps have yet to be reinstated, although some have. (See update below for a response from Good Reads.)

Application Insights, the new analytics tool that the engineer described, is not the only new feature that Facebook is rolling out in the coming weeks: it is also gearing up to make Facebook Credits into the only form of virtual currency that will be usable by apps on its site.

Project Spartan has been linked to Facebook’s bigger goals of taking its site more fully on to mobile platforms. The idea, reportedly, is to create a fully functional mobile web site for the social network that will let users engage in all the apps on the site — which currently do not appear in Facebook’s apps — in a way that bypasses Apple’s own payment (and commission) system. Some have also suggested that it could also tie in with the other big area that Facebook is apparently looking to tap: music, with deals with the likes of Spotify reportedly imminent.

All of this points to a significantly bigger, but more controlling, Facebook than we have seen yet. But it also is a warning sign of what problems Facebook could have to its business model if it doesn’t play its cards right:

Many of the developers were surprised by the blocks because up to that point they claimed good ratings from their apps, and little in the way of user complaints: the spam alerts, it seems, were related to how other users — Facebook friends of those registered with the apps — were filtering out updates from the apps in question. But rather than give the developers a chance to modify how they messaged people, Facebook instead cut off the apps altogether.

It may be the case with all big platforms that there will be developers who complain about how responsive the platforms can be to problems or complaints. But as Facebook grows it will have to make sure that this frustration does not grow into outright departure, a threat that already seems to be coming up: “We sincerely suggest you, fellow developers, to start your business in other platform [sic] as a back up (if you have not done this already),” wrote one developer on a forum.

Update: We had a response from Good Reads that provides a first-hand look of one company that ran foul of Facebook’s new filters, and how it got back in its good books (pun intentended..). Otis Chandler, the CEO of Good Reads tells us by email:

“We were shut down on Thursday around 6pm. We appealed, and were rejected Friday morning, and told to create a new app, sacrificing nearly a million installs we’d built up over four years.

We didn’t know the reason we were shut down, but audited our app and cleaned up a few things just to be sure, and appealed again. We were happily restored friday late afternoon. A great reminder of the power Facebook has over all of us developers.”